Title: Sequence-based pathogen discovery in post-stem cell transplantation syndromes Applicant: Ami S. Bhatt, MD, PhD, Dana-Farber Cancer Institute and Harvard Medical School Mentor: Matthew Meyerson, MD, PhD, Dana-Farber Cancer Institute, Harvard Medical School, and Broad Institute While the clinical application of allogeneic hematopoietic stem cell transplantation (HSCT) has resulted in the ability to cure otherwise refractory hematologic diseases, there is a significant rate of treatment-related morbidity and mortality. Patients who have undergone stem cell transplantation are highly susceptible to life- threatening infections; while the pathogenic trigger is known in a subset of these cases, in many other potentially infectious syndromes the trigger remains elusive. This proposal seeks, through an innovative, translational and integrated research program, to characterize the gastrointestinal and pulmonary microbiome in healthy and diseased patients who have undergone allogeneic stem cell transplantation, thus allowing for unbiased, sequencing-based identification of potential pathogens. This approach has been validated in the investigation of the gastrointestinal microbiome as demonstrated by my preliminary data, where I have successfully employed a sequencing and computational method for the identification of a new bacterium, Bradyrhizobium enterica, in a post-HSCT colitis syndrome. I intend to culture and isolate this organism and undertake validation experiments whereby the pathogenicity of B. enterica will be investigated in a murine model of infectious colitis. I will also use the sequencing-based methodology that we have developed in order to investigate the pulmonary microbiome of patients with post-HSCT idiopathic pneumonia syndrome and bronchiolitis obliterans, two post-HSCT pulmonary syndromes that are posited to be triggered by a heretofore- unidentified pathogen. In doing so, we hope to illuminate the triggers of these idiopathic illnesses and translate this knowledge into future targeted therapies. I am a senior hematology/oncology fellow at the Dana-Farber Cancer Institute and have substantial prior research experience in biochemistry and molecular biology. I am currently engaged in a mentored research project as in the laboratory of Matthew Meyerson at the Broad Institute and DFCI. Taking advantage of the excellent research environment at Dana-Farber Cancer Institute and Broad Institute, I intend to learn modern genomic and bioinformatics techniques and to apply them to comprehensively define microbial alterations that may contribute to cancer treatment-related morbidity and mortality. I am seeking a K08 award to support mentored research so that I may become facile with the use of modern tools for genomic and metagenomic analysis of diseased human tissues and so that I may learn how to functionally validate promising candidate pathogens to demonstrate disease-association and causation. I will also be co-mentored by Dr. Wendy Garrett, a well-respected, R01-funded translational oncologist at with expertise in the generation and manipulation of mouse models of human colitis syndromes. She will advise me in selecting appropriate cell-based and animal models in which to test candidate pathogens identified by the aforementioned genomic approaches, and will oversee these animal-based experiments. I am supported by my institution in my plan to devote 80% of my time to a focused research program in understanding the pathogenic perturbations of the microbiome after hematopoietic stem cell transplantation. I will complement this with 20% of my effort dedicated to seeing patients who have undergone hematopoietic stem cell transplantation in the clinic and to training activities including attendance and presentation at internal and external seminar series and meetings as well as independent coursework in the tools of translational investigation and modern genomic analysis. My ultimate goal is to become an independent physician-scientist with a tenure-track position at an academic cancer center with a research effort focused on complications of hematopoietic stem cell transplantation and the use of modern genomic techniques to identify new human pathogens.